Contacts of the helix formed by residues 444 - 459 (chain D) in PDB entry 3U1K
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 444 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D ILE* 6.2 0.2 - - - -
429D PHE 5.6 1.2 + - - -
439D LYS 5.8 2.0 + - - -
443D LEU* 1.3 80.0 - - + +
445D ARG* 1.3 61.0 + - - +
446D ARG* 3.0 27.7 + - - +
447D GLU* 3.1 45.2 + - - +
448D LEU* 3.1 21.9 + - - +
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Residues in contact with ARG 445 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D VAL* 4.7 8.3 - - - +
100D VAL 3.2 19.8 + - - +
101D ASP* 3.7 18.5 + - - +
102D TYR 5.3 0.8 + - - -
123D THR* 4.8 9.9 - - - +
127D GLU 4.7 0.2 + - - -
128D ILE* 3.8 43.7 - - + +
131D SER* 3.4 30.0 + - - -
132D ARG* 3.6 24.4 - - - +
443D LEU 3.2 11.0 + - - +
444D ASN* 1.3 73.1 + - - +
446D ARG* 1.3 58.0 + - - +
448D LEU* 3.3 4.9 + - - +
449D GLY 3.0 22.0 + - - -
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Residues in contact with ARG 446 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D CIT 3.2 44.6 + - - +
132D ARG* 3.5 10.3 - - - +
427D TYR* 5.9 0.2 - - + -
429D PHE* 3.2 40.4 - - - +
444D ASN* 3.0 16.7 + - - +
445D ARG* 1.3 76.6 - - - +
447D GLU* 1.3 62.8 + - - +
449D GLY* 3.3 0.7 + - - -
450D HIS* 2.9 45.9 + - + +
670D CIT 3.2 25.7 + - - -
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Residues in contact with GLU 447 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426D HIS* 5.9 1.0 - - - -
427D TYR* 3.5 33.4 + - + +
428D GLU* 3.6 13.4 - - - +
429D PHE* 2.7 47.1 + - + +
430D PRO* 5.1 0.5 - - - +
444D ASN* 3.1 43.3 + - + +
446D ARG* 1.3 78.2 - - - +
448D LEU* 1.3 59.4 + - - +
451D GLY* 2.9 26.9 + - - -
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Residues in contact with LEU 448 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D ASP* 3.8 42.6 - - + +
128D ILE* 4.6 17.7 - - + -
129D LEU* 4.0 25.4 - - + -
444D ASN 3.1 14.5 + - - +
445D ARG* 3.5 11.9 - - - +
447D GLU* 1.3 76.8 - - - +
449D GLY* 1.3 57.8 + - - +
451D GLY* 3.7 0.7 - - - -
452D ALA* 2.9 27.4 + - + +
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Residues in contact with GLY 449 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129D LEU* 3.9 18.6 - - - +
132D ARG* 4.0 14.3 - - - +
445D ARG 3.0 14.5 + - - -
446D ARG 3.6 3.1 - - - -
448D LEU* 1.3 77.1 - - - +
450D HIS* 1.3 58.7 + - - +
452D ALA* 3.2 3.5 + - - +
453D LEU* 3.0 28.6 + - - +
558D GLN* 4.7 7.1 + - - -
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Residues in contact with HIS 450 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D CIT 2.6 38.1 + - - -
132D ARG* 4.3 3.8 - - - -
427D TYR* 3.0 47.7 + - + -
446D ARG* 2.9 36.4 + - + +
449D GLY* 1.3 70.7 - - - +
451D GLY* 1.3 64.4 + - - +
453D LEU* 3.3 5.6 + - - +
454D ALA* 3.0 24.9 + - - +
484D SER* 4.0 10.0 - - - -
546D LYS* 4.5 3.6 - - - -
558D GLN* 4.5 2.9 - - - -
670D CIT 2.9 45.3 + - - -
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Residues in contact with GLY 451 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425D LEU* 3.9 18.0 - - - +
427D TYR* 3.4 25.6 - - - +
447D GLU 2.9 15.4 + - - -
448D LEU* 3.7 1.3 - - - -
450D HIS* 1.3 73.5 - - - +
452D ALA* 1.3 65.1 + - - +
453D LEU 3.2 0.2 + - - -
454D ALA* 3.3 1.6 + - - -
455D GLU* 2.9 25.6 + - - +
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Residues in contact with ALA 452 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D LEU* 3.8 31.6 - - + -
448D LEU* 2.9 22.7 + - + +
449D GLY 3.2 4.2 + - - +
451D GLY* 1.3 72.7 - - - +
453D LEU* 1.3 62.4 + - - +
455D GLU* 3.6 11.1 - - - +
456D LYS* 3.0 32.6 + - + +
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Residues in contact with LEU 453 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449D GLY 3.0 13.4 + - - +
450D HIS* 3.6 7.9 - - - +
451D GLY 3.1 0.2 - - - -
452D ALA* 1.3 74.7 - - - +
454D ALA* 1.3 66.2 + - - +
456D LYS* 3.3 26.9 + - - +
457D ALA* 3.0 23.1 + - - +
484D SER* 3.7 22.9 - - - +
485D MET* 3.7 20.0 - - + -
546D LYS* 4.2 8.1 - - + +
556D ALA* 4.0 17.3 - - + -
557D LEU 4.3 4.5 - - - -
558D GLN* 3.8 49.1 - - + +
670D CIT 4.7 0.2 - - - +
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Residues in contact with ALA 454 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425D LEU* 3.9 22.4 - - + -
427D TYR* 5.7 0.4 - - + -
450D HIS 3.0 16.4 + - - +
451D GLY 4.0 2.2 - - - +
453D LEU* 1.3 77.2 - - - +
455D GLU* 1.3 62.1 + - - +
457D ALA* 3.2 17.5 + - - +
458D LEU* 3.3 18.0 + - - +
484D SER 3.9 21.5 + - - +
485D MET* 5.4 0.7 - - - -
487D SER* 4.0 12.8 - - - -
488D ALA* 4.0 6.9 - - - +
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Residues in contact with GLU 455 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419D LYS* 3.0 30.0 + - - +
423D PHE* 3.6 21.6 - - + -
424D MET* 3.2 15.8 - - - +
425D LEU* 3.0 45.0 + - + +
451D GLY 2.9 18.6 + - - +
452D ALA* 3.6 10.5 - - - +
454D ALA* 1.3 77.1 - - - +
456D LYS* 1.3 59.3 + - - +
458D LEU 3.0 2.3 + - - -
459D TYR* 2.8 28.8 + - + +
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Residues in contact with LYS 456 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230D GLU* 2.6 36.0 + - - +
231D ALA 3.0 33.7 + - - -
232D SER* 3.9 22.4 + - - +
452D ALA* 3.0 21.9 + - + +
453D LEU* 3.3 25.5 - - - +
455D GLU* 1.3 76.2 - - - +
457D ALA* 1.3 64.0 + - - +
459D TYR* 3.9 11.2 - - + +
460D PRO* 3.3 17.2 - - - +
555D THR 3.5 10.2 - - - +
556D ALA* 4.0 8.3 - - + -
557D LEU 4.1 0.2 + - - -
558D GLN* 5.0 0.2 - - - +
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Residues in contact with ALA 457 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453D LEU 3.0 13.6 + - - +
454D ALA* 3.3 11.9 - - - +
455D GLU 3.2 0.2 - - - -
456D LYS* 1.3 77.1 - - - +
458D LEU* 1.3 59.9 + - - +
460D PRO* 3.8 0.2 - - - +
485D MET* 5.4 1.8 - - + -
488D ALA* 4.1 14.4 - - + -
506D VAL* 3.7 13.0 - - + +
548D ALA* 3.8 27.4 - - + -
555D THR* 2.7 30.0 + - - +
556D ALA* 3.7 7.2 - - + -
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Residues in contact with LEU 458 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423D PHE* 3.7 19.5 - - + -
425D LEU* 3.8 24.0 - - + -
454D ALA 3.6 13.9 - - - +
455D GLU 3.0 6.3 + - - +
457D ALA* 1.3 75.7 - - - +
459D TYR* 1.3 68.6 + - - +
460D PRO* 3.1 5.8 - - - -
461D VAL* 3.1 25.9 + - + +
462D ILE* 3.4 6.0 - - - +
472D VAL* 5.1 0.9 - - + -
488D ALA* 3.5 30.1 - - - +
491D GLY* 4.0 13.5 - - - -
492D SER* 3.8 13.9 - - - +
495D LEU* 4.3 10.8 - - + -
506D VAL* 3.7 26.0 - - + -
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Residues in contact with TYR 459 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234D GLU* 3.5 22.7 - - - -
420D ASP* 2.1 59.4 + - + +
421D LYS* 2.8 42.8 + - + -
423D PHE* 4.1 14.8 - + + -
455D GLU* 2.8 19.3 + - + +
456D LYS* 4.1 9.4 - - + -
458D LEU* 1.3 76.8 - - - +
460D PRO* 1.3 68.6 - - + +
462D ILE* 3.0 17.2 + - - +
464D ARG* 4.2 1.9 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il